Fix bug 281734, thanks to Justin Lecher (jlec)

(Portage version: 2.2_rc30/cvs/Linux x86_64)

3 files changed, 38 insertions, 14 deletions

diff --git a/sci-biology/clustalw/ChangeLog b/sci-biology/clustalw/ChangeLog
index c3a51c4b741c..59d7abecdb7e 100644
--- a/sci-biology/clustalw/ChangeLog
+++ b/sci-biology/clustalw/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/clustalw
 # Copyright 2000-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalw/ChangeLog,v 1.16 2009/04/28 23:57:43 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalw/ChangeLog,v 1.17 2009/08/18 15:41:51 weaver Exp $
+
+*clustalw-1.83-r3 (18 Aug 2009)
+
+  18 Aug 2009; Andrey Kislyuk <weaver@gentoo.org>
+  +files/1.83-as-needed.patch, -clustalw-1.83-r2.ebuild,
+  +clustalw-1.83-r3.ebuild:
+  Fix bug 281734, thanks to Justin Lecher (jlec)
 
 *clustalw-2.0.11 (28 Apr 2009)
 
diff --git a/sci-biology/clustalw/clustalw-1.83-r2.ebuild b/sci-biology/clustalw/clustalw-1.83-r3.ebuild
index 03de96f97d1e..1c24269955ce 100644
--- a/sci-biology/clustalw/clustalw-1.83-r2.ebuild
+++ b/sci-biology/clustalw/clustalw-1.83-r3.ebuild
@@ -1,8 +1,10 @@
-# Copyright 1999-2008 Gentoo Foundation
+# Copyright 1999-2009 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalw/clustalw-1.83-r2.ebuild,v 1.1 2008/08/27 22:51:42 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalw/clustalw-1.83-r3.ebuild,v 1.1 2009/08/18 15:41:51 weaver Exp $
 
-inherit toolchain-funcs
+EAPI="2"
+
+inherit base toolchain-funcs
 
 DESCRIPTION="General purpose multiple alignment program for DNA and proteins"
 HOMEPAGE="http://www.embl-heidelberg.de/~seqanal/"
@@ -10,24 +12,22 @@ SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/${PN}${PV}.UNIX.tar.gz"
 
 LICENSE="clustalw"
 SLOT="1"
-KEYWORDS="alpha amd64 ppc ppc64 sparc x86"
+KEYWORDS="~alpha ~amd64 ~ppc ~ppc64 ~sparc ~x86"
 IUSE=""
 
 S="${WORKDIR}"/${PN}${PV}
 
-src_unpack(){
-	unpack ${A}
-	cd "${S}"
+PATCHES=(
+	"${FILESDIR}"/${PV}-as-needed.patch
+)
+
+src_prepare() {
+	base_src_prepare
 	sed -i -e "s/CC	= cc/CC	= $(tc-getCC)/" \
-		-e "s/CFLAGS  = -c -O/CFLAGS  = -c ${CFLAGS}/" \
-		-e "s/LFLAGS	= -O -lm/LFLAGS	= -lm ${CFLAGS}/" makefile || die
+		makefile || die
 	sed -i -e "s%clustalw_help%/usr/share/doc/${PF}/clustalw_help%" clustalw.c || die
 }
 
-src_compile() {
-	emake || die
-}
-
 src_install() {
 	dobin clustalw || die
 	dodoc README clustalv.doc clustalw.doc clustalw.ms
diff --git a/sci-biology/clustalw/files/1.83-as-needed.patch b/sci-biology/clustalw/files/1.83-as-needed.patch
new file mode 100644
index 000000000000..62b4654cddea
--- /dev/null
+++ b/sci-biology/clustalw/files/1.83-as-needed.patch
@@ -0,0 +1,17 @@
+--- makefile	2003-01-29 09:53:45.000000000 +0100
++++ makefile.new	2009-08-17 08:33:16.000000000 +0200
+@@ -11,11 +11,11 @@
+ HEADERS = general.h clustalw.h
+ 
+ CC	= cc
+-CFLAGS  = -c -O
+-LFLAGS	= -O -lm 
++CFLAGS  += -c
++LIBS	= -lm 
+ 
+ clustalw : $(OBJECTS) amenu.o clustalw.o
+-	$(CC) -o $@ $(OBJECTS) amenu.o clustalw.o $(LFLAGS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJECTS) amenu.o clustalw.o $(LIBS)
+ 
+ interface.o : interface.c $(HEADERS) param.h
+ 	$(CC) $(CFLAGS) $*.c